Phylogenetic Analysis of Lauraceae Genomes

The Lauraceae is a pantropical family of flowering plants comprising some 2,500–3,000 species across roughly 50 genera, many of which are of major ecological and economic importance. Phylogenetic analyses of Lauraceae genomes have harnessed advances in high-throughput sequencing, enabling assembly of whole chloroplast genomes and chromosome-level nuclear assemblies. Comparative studies reveal conserved quadripartite plastome structures punctuated by lineage-specific expansions, contractions and gene losses. Phylogenomic approaches, integrating nuclear, plastid and mitochondrial data, have shed light on deep divergences within the Magnoliids, revealing ancient whole-genome duplication events and episodes of incomplete lineage sorting. At finer scales, analyses of hypervariable intergenic spacers and simple sequence repeats have clarified relationships within enigmatic genera such as Neocinnamomum, Sassafras and Ocotea. Insights from these studies underpin improved taxonomic delimitation, inform conservation of keystone tree species and illuminate the assembly of tropical and subtropical forest biomes.

Research from Nature Portfolio

A chromosome-level assembly of the Litsea cubeba nuclear genome, complemented by low-coverage genomic and transcriptomic sampling of diverse Lauraceae taxa, has revealed an ancient whole-genome duplication predating the divergence of Laurales and Magnoliales, followed by lineage-specific duplications in three laurel clades. Phylogenomic discordance at the base of magnoliids was attributed to incomplete lineage sorting, while the evolution of panicle architecture was linked to the FUWA gene family and the diversification of monoterpene synthases was functionally validated, elucidating the genetic basis of floral form and scent production.

The first complete chloroplast genomes of seven Ocotea species have demonstrated remarkably low sequence divergence across Neotropical and Macaronesian lineages. Two hypervariable regions in the large single-copy region and three in the small single-copy region were identified, and simple sequence repeat counts were shown to correlate with breeding systems. A preliminary plastome phylogeny positions Ocotea as sister to a broadly defined Cinnamomum, underscoring close intergeneric relationships within the core Laureae.

Phylogenetic Analysis of Lauraceae Genomes publication trend

The graph below shows the total number of articles in phylogenetic analysis of lauraceae genomes across all publications each year (not limited to Nature Index journals).

Technical terms

Plastome: The complete DNA sequence of a plant’s chloroplast genome, typically arranged in two inverted repeats separated by single-copy regions.

Whole-genome duplication (WGD): An event in which an organism’s entire set of chromosomes is duplicated, often driving evolutionary novelty and speciation.

Inverted repeat (IR): Identical or nearly identical sequences in reverse orientation that flank single-copy regions of the plastome and contribute to structural stability.

Single-copy regions (LSC/SSC): Large (LSC) and small (SSC) segments of the chloroplast genome that each contain unique coding and non-coding sequences.

Simple sequence repeats (SSRs): Short tandemly repeated DNA motifs found throughout the genome, mutable and useful as genetic markers in phylogeographic and population studies.

References

1. The Litsea genome and the evolution of the laurel family. Nature Communications (2020).
2. A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. Scientific Reports (2022).
3. Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). Frontiers in Plant Science (2023).
4. New insights into the plastome evolution of Lauraceae using herbariomics. BMC Plant Biology (2023).
5. Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests. BMC Plant Biology (2022).